Bugs in the System
by liketheriver
Summary: Weir POV as Atlantis is once again on the verge of destruction with only our favorite boys to save the day. SheppardMcKay friendship. One-shot (complete)


_RATING: PG-13 for language._

_SEASON: First season after Before I Sleep and just scant days before Brotherhood_

_MAJOR CHARACTERS: Weir POV with plenty of Sheppard and McKay interaction and a bit of Zelenka, Grodin, and a smidge of Teyla, Beckett, and Kavanaugh. Ford only gets mentioned but is still well loved._

_CATEGORY: Action/humor/angst_

_SUMMARY: Weir POV as Atlantis is once again on the verge of destruction with only our favorite boys to save the day. One-shot (complete)_

_SPOILERS: Rising, 38 Minutes, The Storm, The Eye, Hot Zone, Before I Sleep._

_FEEDBACK: Yes, please. I thrive on it and so do the bunnies._

_DISCLAIMER: I don't own them because if I did I would know how all the technocrap works. I would also give Weir a personality, which is what I have tried to do here._

_NOTES: This is another of my "Outside Looking In" POV stories that follows the McKay/Sheppard friendship as established in my story "Tokens." It is a follow up to "Sentry Duty", "Games", and most importantly "Casting Stones". Although it is technically a one-shot, you should go back and read the others if you haven't as some of the jokes will make more sense. Who knows, you might even enjoy yourself!_

_ACKNOWLEDGEMENTS: This story has not been Beta-ed, mainly because I don't have one. So, all mistakes are mine. For all those wanting more POV, the bunnies are there, just need a little more care and feeding. Reviews always help! Thanks to everyone who read and reviewed the other stories-whenever I have a bad day at work I go back and reread them in order to convince myself of my god-like standing in the world. lol! Seriously, you are all too kind and as always- this is all your fault. _

**Bugs in the System**

**by Liketheriver**

"Oh, no."

It is the simplicity of the statement that causes the icy hot prickles to rise on my skin. No sarcasm, no over the top anger, no pompous attitude or belittling sting, nothing that would suggest that Rodney had just uttered those two little words.

"McKay?" John calls to the scientists over the radio. I can see the worried crease that appears on his brow that mirrors my own. "What's wrong?"

"The doors just sealed shut," he says all too calmly, "and the pumps have started."

I'll admit that the day had not started out well at all. No, the Wraith were not beating down the door, yet. The Genii hadn't tried to take over the city, again. And no fights had broken out over the last packages of ho-hos, so far. No nothing so panic inducing as any of those, just one of my most dreaded jobs as expedition commander, doling out the discipline, playing the bureaucrat and maintaining the system.

People would think that being the commander on an expedition to an entirely different galaxy would be full of new and exciting challenges. And on a certain level, they would be correct. We have encountered our fair share of alien cultures, some friendly, others not. We have discovered a plethora of new technologies, some life saving, some intriguing, some just down right weird, and a fare number still mysteries. And we have had more than enough death defying moments, all of which I would gladly trade for the mundanely more common administrative requirements that take up the vast majority of my time.

Don't get me wrong, I was perfectly aware when I took this command that everything wouldn't be dazzling technological advancements and interesting new societies. I knew that I would be responsible for the management of the entire crew and the politics of interpersonal relationships that would follow. Still, this group of brilliant and brave scientists and soldiers has been more of a challenge than I could have ever imagined.

Perhaps it is a touch of island madness. Although the city is roughly the size of Manhattan, for safety I try to limit unofficial excursions beyond the primary hub of base activity, so that everyone is stuck in a relatively small area. Perhaps it the mix of expedition personnel and their particular talents and accompanying personalities. Perhaps it is the fact that we are trapped here for the time being with no obvious way home. Perhaps it is a combination of all these things, but some of the problems that have arisen never occurred to me even in my wildest dreams.

Just two weeks ago, security woke me in the middle of the night to handle a dispute that had arisen between two of the crew over, of all things, a game of strip chess. I came to my office to find two scantly clad scientists yelling at each other. Once I got them to finally calm down, the female team member informed me that the dispute had arisen because her male competitor had tried to use the King's Indian Defense, even though that had been expressly forbidden during the pre-game establishment of rules. I challenge General O'Neill to one up me on that one. I confiscated the game for one week and sent them to their respective quarters.

Then there was the incident with the last can of peaches, or at least what someone mistakenly claimed was the last can of peaches. Honestly, I have worked disaster recovery efforts in underdeveloped countries where people who have not had clean water in three days behaved more rationally than the crew when they thought the last can of peaches had been eaten. Since then, I have had the sacred industrial-sized can displayed very prominently in the cafeteria with orders that it is not to be opened unless by express direction from myself. As far as I am concerned, we will be eating bark and twigs seasoned with nothing more than the tiny MRE Tabasco bottles before that can is ever opened.

And don't even get me started about the uproar that happened when the chemistry staff hoarded away an entire pallet of toilet paper. I thought the physicists where going to mount an all out offensive and they probably would have if they had been more successful in their negotiations with the biologists. Fortunately, the biologists were as distrustful of the physicists as they were the chemists and I was able to have Sgt. Bates' men secure the precious commodity before a formal declaration of war could be issued.

The military contingent, although not as reactionary to the loss of luxuries and conveniences as the scientists, have had their own set of challenges. They tend to be more rough and tumble in nature. Sure, the occasional brawl has broken out, but Sgt. Bates and Major Sheppard have been very good about keeping those to a minimum. And we even have one young lieutenant that is now commuting between the base and the mainland after marrying a striking Athosian girl- the baby that led to the sudden nuptials is due in a few months. I don't even want to think about the immigration paperwork that will have to be filed when we finally return to Earth. No, the biggest challenge has been keeping them occupied on base.

Over the years, I have come to understand the saying 'idle hands are the devil's playthings.' That is especially true for the men and women of the armed services that have accompanied us to Atlantis. We are completely dependent on them for our protection, but let's face it, until the dreaded day that the Wraith actually appear, they are limited to occasional excursions through the stargate and breaking up coups involving paper products and the scientists.

Major Sheppard has decided to employee a strategy that he was subjected to in the Middle East, perpetual movement of supplies. He told me once about having to load and unload the same truck over a dozen times in one week, for no other purpose that he could perceive than simply keeping the troops busy. We have begun the same method here, moving supplies, equipment, and other sundries from one designated storage room to another. I have found that the benefit it two fold- it keeps the troops occupied and it makes it harder for the science staff to locate the stash of toilet paper.

Given these other daily challenges, you would think that a simple disciplinary meeting would be a piece of cake. And normally it would, except for the two men sitting and waiting to receive their punishment.

I opened the files in front of me and pretended to study them, while in reality I looked up from under my eyebrows at my military and scientific advisors. Major John Sheppard chewed on the inside of his lower lip as he sat with his arms crossed over his chest. Sat, however, may have been too formal a description for his stance. It was a full blown slouch so that his head was almost resting on the back of the chair. In contrast, the posture of his partner in crime, Dr. Rodney McKay, would have made any charm school matron proud. Straight backed and attentive with hands folded in his lap, his discomfort was betrayed only by the constant tapping of one foot and the glint of annoyance that he couldn't hide in his blue eyes.

I could not help but be struck by how different these two men are from appearance to personality. The one dark and dry, brooding and sarcastic; the other light and animated, opinionated and biting. It is like comparing Guinness to a gimlet; dark chocolate to sweet tarts, so striking is their polarity. And all of which are an acquired taste. I had decided long ago that I would have problems with these two, but not for the reasons that I found on my desks that morning. No, early on, I thought they would have killed each other by now. Instead they have become good friends and that has lead to some entirely unexpected challenges for me. I can't help but find that amazing and on some level, amusing. Still, I have to admit that my initial assessment was based on first impressions, and really, neither of them makes a very good first impression. Why do you think Teyla is on their first contact team? The warnings I received from the SGC didn't help bolster my opinion. Colonel Carter had made it incredibly clear that although Dr. McKay was a competent scientist, his personality, or in her words, lack there of, would be a challenge to any mission commander. General O'Neill and Colonel Sumner had been just as forewarning about Major Sheppard's lack of respect for authority.

But, what was I to do? Given a choice, maybe I wouldn't have brought either man based on the portents offered. But that was just the problem, there was no choice. Aside from Samantha Carter, no one knows more about the Stargate than Rodney McKay, and no one anywhere knows more about Ancient technology than the man. And the Ancient's gene that has manifested so strongly in John Sheppard made him an invaluable asset worth the risk So, I confess, I brought the two of them along for purely perfunctory reasons; if the mission was to succeed I would need both of these men and I would deal with the ramifications later. Since that time, however, both of them have proven themselves more valuable than anyone, even I, could imagine. Acting individually, they have each saved my life from the same man on the same day; one by stepping in front of the receiving end of a gun, and the other by working the delivering end of one. And together they have saved their teammates and all of Atlantis numerous times. Little did I know at the time that they were just moments from being called on to do it again.

"First, let me start off by saying that your work and dedication to this mission have been exemplary. I could not be more pleased by the strides we have made in learning about the Ancient's and their technologies and the contacts we have made with other cultures in the Pegasus Galaxy. All of which are a direct result of your contributions and dedication to this expedition."

Major Sheppard sat up slightly and rolled his hands at me, "But…?"

I took a breath and continued on. "But, you are two of my lead advisors, two of the highest ranking personnel on the expedition, and as such, I expect you to set an example for the other mission personnel to follow." I ignored the snort and escalated foot tapping from Rodney and continued. "There have been several incidents brought to my attention, both from recent missions and on base…"

"Kavanaugh," Rodney sneered the name in way of interruption, "I swear to God, I am going to get me a pair of scissors as soon as we are done here and…"

Before I could regain control of the conversation, the alarms started to sound. The difference between the alarms here on Atlantis and those at the SGC is one of the most striking divergences I have come across. Back on Earth, every incoming wormhole is greeted with a teeth rattling klaxon. I swear, they had me jumping to duck and cover every time they sounded the first week I was in the Mountain. By the sound of those sirens, you would think that every team returning to Earth was bringing the Four Horsemen followed by a slew of Jaffa fast on their heels.

But here, the alarms give me the odd impression of a goose trying to sneeze. They seem less distressful than their Earthly cousins, almost polite. As if the city were saying, 'Oh, excuse me, but if you have the time, you might want to come and see what disaster is about to befall you." And yet it is the rarity of them that sets my nerves on edge when they sound.

At the noise, the three of us exchanged quick worried glances and, wordlessly, we all moved from my office to the control room outside. Dr. Peter Grodin was studying the controls and displays on the consoles. He looked up and addressed me as soon as I entered the room. "It appears to be a fire alarm for part of the unoccupied section of the city." A blinking dot materialized on one of the displays, showing where the fire was located.

"Dispatch a team to investigate," I directed Peter, then turned to Rodney. "Does the city have a fire suppression system?"

"We think so," he responded.

John gave him a disapproving look, "You think?"

"Did you want me to start a fire to test the theory? It's never come up before," he defended.

Although not technically a military issue, the team dispatched to investigate and contain the fire would be military personnel. "Major,…" I started.

"On it," he acknowledged as he turned to leave and then over his shoulder he called to Rodney, "McKay, we're going to have to have a little chat about all these things that we're using around here without knowing how they work."

"Fine," he called back as he punched keys on the console in front of him, "you find the instruction manuals and I will be thrilled to go over them with you."

I stood in the control room with Rodney, listening to the alarms graciously honk and waiting for a report on the fire. After several minutes, the Major came across the radio. "Are you sure about the location of the fire?"

"Positive," Dr. Grodin responded as we watched the life signs detector on the display, "it should be right around the next corner."

"It's just that there isn't any smoke." The dots representing the team of firefighters converged with the blinking alarm dot. "There's nothing here."

"Are you sure?" Rodney asked.

"Hmmm, no smoke, no flames, no heat, no Girl Scouts singing Kumbaya. I'm pretty sure that means no fire, Rodney."

Rodney rolled his eyes as I addressed him, "Do you think it was a false alarm?"

"Possibly, although I've never seen a false alarm on any of the Ancient's systems before."

I nod my agreement then call back over the radio. "Major, can you tell if maybe it is in walls or floor…." I silenced at the same time the alarms did.

"Did you do that?" John asked as the alarms also stopped in his location.

"I was just going to ask you the same thing," I admitted.

"Hmmm," was his simple response. "Crisis averted?"

I looked to Rodney who gave me an indecisive shrug. "Major," I directed, "stay in your position and monitor the area for the next half hour."

"Copy that," he said and then was gone from the frequency.

I then turned to my two scientists. "See what you can find in the system that might have caused a false alarm."

Before either could respond, I heard a very irate Czechoslovakian coming down the hall. "But you cannot simply take my laptop, it is mine, I have need of it!"

Dr. Kavanaugh actually held the subject computer above his head, like an older child taunting a younger sibling with a favored toy. "I told you, mine just collapsed on me this morning. I was lucky that I was able to download my files into the main system before I lost everything and I need a computer to download more files on the nanoresearch that was taking place on PX9467. Besides, it's not your laptop, it's the expeditions, and the expedition needs me to take this back to the planet and gather more data."

"Oh, and I am to suppose your research is more important than my own?" Dr. Zelenka demanded

"Yes."

Dr. Kavanaugh's egotistical reply was met by a stream of Slavic insults the likes of which I hadn't heard since,…well, since the Czech himself had stood in my office two weeks ago in little more than his skivvies, justifying his use of the King's Indian Defense.

I stepped in to intervene. "Gentlemen, is there a problem I should be aware of?"

Both men looked like children with their hands caught in the cookie jar. Dr. Zelenka took a step back, lowering his head as if the question alone had chastised him, or maybe it was the fact that I knew we wore red bikini underwear. Dr. Kavanaugh plastered one of his fake smiles across his face that had become almost trademark since our argument over the disabled jumper caught in the wormhole. "Dr. Weir, I am scheduled to head back to PX9467 in five minutes and my computer isn't functioning. The whole trip will be pointless if I don't have a laptop to download files onto."

"And so you just decided to take Dr. Zelenka's?"

"It was handy, I was in a hurry, and it wasn't until just now that I realized it was actually his."

'Right', I thought silently. You don't make a living sitting in a room full of foreign diplomats negotiating trade treaties and not learn to recognize bullshit when you hear it. But you do learn how to work the system to make it seem that everyone gets what they want. Because if you don't work the system, it will work you.

"Dr. McKay, do you have a computer that Dr. Kavanaugh can use for his trip?"

Rodney was busily analyzing the main systems and didn't even look up. With a irritated sigh he replied, "Bottom shelf on my work bench, but I want it returned as soon as he is back."

I could tell the thought of helping out his arch nemesis grated Rodney to no end, but he was busy and would soon forget about it. Zelenka would get his computer back, Kavanaugh would get a loaner for his trip, and I would get Kavanaugh through the wormhole and on the other side of the galaxy for the rest of the day. See, everybody's happy.

Kavanaugh soon returned with his borrowed laptop and joined Sgt. Stackhouse and the rest of his team in the gate room. After their last disastrous trip to the planet, Team 1 had graciously declined going back. Seeing as Lt. Ford was still hobbling around in a leg brace probably contributed heavily to the decision. Peter prepared to dial the address, but stopped with a scowl on his face. "Rodney?" he called.

"What now?" came the impatient reply.

"The shield won't lower."

"What do you mean, the shield won't lower?"

"Just that. I went to dial the address on the DHD, but I can't get the shield to disengage."

Dr. McKay left the console he had been working and went to the DHD by Dr. Grodin. He punched the same commands that Peter had just tried. At the same time, the alarms started sounding again.

"Oh, you have got to be kidding me," Rodney exclaimed to the room in general.

Peter turned to the displays, "Another fire alarm, this time two floors up from the last one."

Major Sheppard came across again, "Please tell me that isn't what I think it is."

"Major, we are showing a fire two floors up from your current location," I informed him.

"We'll check it out," he told me in a disgruntled tone.

At the same time, another blinking dot appears on the map, this time on the North Pier. "Now it says there is flooding on the North Pier," Peter explained.

"Major Sheppard?" I called.

A frustrated, "On my way," answered back.

"Rodney, any ideas about what it going on here?" I tried to keep the concern from creeping into my voice.

"It's as if the safeguards are all malfunctioning, like they have all gone cattywonkous."

"Is that the technical term, McKay?" John asked across the radio.

"No, but it's the polite term for what I would really like to say." He addressed me again. "All the systems seem to be crashing." His expression changed and it was as if I could see the cartoon light bulb click on above his head. "Just like Kavanaugh's computer." He ran down the hall. "I'll be right back."

An hour later we sat in the briefing room. After chasing down over a dozen various fire and flood alarms, Major Sheppard had turned the foot work over to Sgt. Bates and joined us. Dr. Zelenka was also present, with Dr. Grodin continuing to monitor the never ending stream of alarms that were still coming in.

"Ends up we did bring a virus back with us from the nanite planet after all," Rodney told us with a self satisfied grin. "Only it wasn't human, it was the computer variety."

"A computer virus, but how?" I asked.

"Kavanaugh's files on the nanotechnology research. When his laptop crashed he downloaded the files to Atlantis' main system and in so doing infected it."

"Kavanaugh," John growled the name.

"Actually, Major, its really not his fault."

"You're defending him?" The Major sounded shocked.

"Well, it's not like Norton's Antivirus is going to catch an alien computer bug. And technically, it's not really a virus, more like a program."

"He downloaded a program from a potentially hostile planet into our system?" I asked in amazement.

"Again, it's not really his fault."

"Stop that!" John ordered. "It's creeping me out. You defending Kavanaugh has got to be one of the signs of the Apocalypse."

"As much as I would normally agree with you, what he did, although careless, would have appeared relatively harmless at the time." He continued his explanation. "He downloaded a file of what appears to be safety procedures for handling various hazardous materials hoping it would have some information pertaining to the nanovirus. In reality, it was a program to activate the various fail safes they had in place at their hazmat facilities on the planet."

"So, just unload the program."

"It is not so simple, Major," Dr. Zelenka cut in. "The program, it is trying to integrate with the Atlantian system. As a result, it appears to be testing various systems, then rewriting them so as to match it's preestablish protocols."

Rodney took up the lecture again, "Now the rewriting itself does not seem to be too serious of a problem. It appears that it is just tweaking them here and there but they are still pretty much functional after all is said and done."

Major Sheppard leaned forward in his seat. "So, what, we wait for it to test all the fire alarm systems, rewrite them, then go back to normal?"

"If only it were that simple. No, the real problem comes in the testing it is doing prior to the rewrite." From our confused looks he gave a frustrated shake of his head as if lecturing to small children. "What is the primary safety feature that the Ancients used to protect Atlantis?"

"They had it rise out of the ocean," John answered confidently.

"No, that was the secondary failsafe put in place to protect the city when the primary feature failed."

"They submerged it in the first place," I said as the dreadful reality settled over me.

"Exactly, Elizabeth! I would give you a gold star but I'm afraid it will just wash away in the imminent rising floodwaters."

"This computer bug is going to sink the city?" Major Sheppard demanded.

"In all likelihood, it is going to try."

"And will it succeed?"

"There's a pretty good chance."

"What's that supposed to mean?"

"What, do you want me to calculate the probability for you? Better than fifty-fifty but less than one hundred percent. Does that help? I just figured out there was a problem, for Pete's sake. I haven't had time to run the statistics."

"But, when the Ancient's did it originally, there was a shield. We don't have the power to put the shields back in place."

"Yes, Major, I know that, hence the sarcastic yet witty rising floodwaters comment."

"Not so witty, Rodney."

"Can we completely shut down the system?" I asked cutting off their exchange. "Like a reboot?"

Dr. McKay shook his head. "Not only would that not remove the program, it could be extremely dangerous. There are literally hundreds of safety protocols and power puffers that are associated with powering up the stargate, many of which are probably already compromised. If we shut it down then turn it back on, we could overload the gate and blow the city up from the inside out."

"How long?" My first priority was to protect the people of the expedition, my second to protect the city.

Dr. Zelenka interjected again. "It appears that it is to be starting with simpler systems first, which is why it is working on fire alarms and gate shield now, but we believe it will eventually move to more complex systems, like quarantine protocol we saw when the nanovirus was released. On plus side, there are probably systems we have not yet discovered, which should maybe buy us more time. The program that submerged the city is probably most complicated, so it should be last one it reaches. Given these assumptions, we believe we have approximately twelve hours, give or take."

I stood and turned to Major Sheppard, "Begin evacuation procedures immediately. I want everyone off the city in six hours or less."

"We will have to take the jumpers to the mainland," Rodney informed me, "seeing as the shields still won't respond on the stargate,"

I nodded, "Very well, get all available pilots to start shuttling as soon as we are done here, except of course you Doctor. I want you working to stop this from spreading any further, and if possible you, Major. I want you to oversee the evacuation and assist Dr. McKay with your ATA gene if necessary."

Everyone began to leave and I grabbed Rodney by the arm. "If the city does sink again, will the failsafe cause it to resurface?"

"Honestly, Elizabeth, we don't know how the failsafe operated in the first place. It could have been powered by a separate ZedPM that was depleted in the process of raising the city, which would mean it was a one time occurrence. If its not, then there is a possibility that the main control system could still house the resurfacing protocol, but that is probably a moot point seeing as being buried in seawater will probably fry the system anyway."

"You do realize that would mean the stargate would be lost under several hundred feet of ocean."

"Unfortunately, that thought had crossed my mind. But I prefer to concentrate on one catastrophe at a time. Besides, the Russians were able to salvage one off the ocean floor back on Earth, who's to say we couldn't either."

I nodded my head with a weak smile. Yes, the Russians had done it with the entire Russian fleet at their beck and call. We would have a handful of jumpers and whatever we could carry on them to the mainland. Not exactly a heartening thought. Still, we would have the ingenuity of all the expedition members and that had been enough to save us in the past, although even the supply of those was decreasing on an almost weekly basis.

So many lives lost, and if I allow myself to be a realist, there will be more lost in the future. Have you ever gone to a movie and knew five minutes after a character is introduced that they will be dead before the second act? It is always the baby-faced soldier, the quirky oddball scientist, or the soft-hearted nurse. Well, I pass those people everyday in the hall, smile hello to them in the cafeteria, listen attentively to their discussions. Everytime we loose someone, a rock settles in my stomach and I can't help but wonder, who will be next?

When the Wraith come, I know we will be outmanned, outgunned, and outright in trouble. Our only hope lies in finding a ZPM. I cannot save this galaxy, but I will do my best to save as many members of my crew as possible and I won't even be able to do that if the city along with the stargate is sitting on the seafloor.

The evacuation went smoothly if a little frantically. Since the team working to stop the virus had been unsuccessful, it took place with the accompaniment of alarms and flashing screens, which did little to help matters. Certainly no repeats of the uproar seen during the Toilet Paper Wars or the Peach Riots of ought five, but the small amount of chaos was really unavoidable. Not that people had a lot of personal items they needed to pack up, but when there is a good possibility that you will never come back, you take everything you can carry. We actually had several jumper runs loaded with nothing more than food supplies, equipment, and survival gear. And I had the expected level of complaining about critical experiments being interrupted and equipment that could not be disassembled in the allotted time that would have to be left behind.

"Dr. Weir," Teyla called from behind me as I explained to a biologist that the tank of fish he was studying would have to remain. "The last of the Athosians are currently boarded on the Jumper about to leave for the mainland. Is there anything that you require of me here on Atlantis?"

Behind us, we could hear John and Rodney trying to work on the computer system.

"I don't think you are thinking at it hard enough."

"I think I'm thinking as hard as I can think, it just won't respond. And no smart ass comments about how hard you think I can think. If you think you can think harder than I can think, then I think you're more than welcome to try."

"Does it want to respond but can't or is it just not responding?"

"Do I look like Dr. Phil here? How am I supposed to know what the system _wants_ to do? Can it even want to do something? All I know is that it won't respond."

"No, Teyla," I told her, "your place is with your people now. You will be of much more use on the mainland than sticking around here."

She looked with a kind of longing at the two men arguing behind us, as if trying to decide if staying with 'her people' actually meant staying with them. Finally, she forced a smile and nodded in agreement. "Perhaps you are right."

She left and the number of personnel still on Atlantis dwindled further. Eventually, the last shuttle was loaded and ready to depart. Dr. McKay and his team had still been unsuccessful in slowing the virus despite all their efforts.

"Major Sheppard, Jumper One is waiting for you in the bay." Dr. Carson Beckett's Scottish brogue came across the radio. "We're taking the last shuttle out now. Dr. Weir, we've saved you a seat."

"They're announcing your flight," the Major told me.

Everyone was gone except myself, Major Sheppard, Dr. McKay and his ever present support team of Drs. Grodin and Zelenka. The station was jarringly quite, even the alarms had settled down, which according to Rodney was not a good sign because it indicated the low hanging fruit was gone and the virus was working on the larger safety systems. I couldn't help but wonder if this was how it was for my alternate self when she was left behind 10,000 years earlier. Like her, I had a duty to fulfill, and that duty was here on Atlantis.

I shook my head, "Thank you, Carson, but I'll be staying here." From his spot at the command console, Rodney looked up. John frowned and started to protest, but I just smiled as I looked him in the eyes. "I'm sure Major Sheppard will find a place for me in his jumper."

"Are you sure about that, then?" he asked. The concern was evident in that beautiful voice of his. It was soothing, comforting, like a warm blanket around your shoulders on a rainy Glasgow afternoon.

"Don't worry," I told him, "I'm in good hands."

"Aye, lass, the best." Carson hesitated then finally spoke. "Alright then, God Speed to the lot of you."

"We'll see you shortly," I told him, then they, too, were gone.

John just continued to frown. "I don't know what you intend to prove by staying here. Going down with the ship, or city, isn't part of your job description."

"Really? Have you read my job description?" I asked him with a smirk.

"Hell, I haven't even read my own. Not that it really matters, because it changes on a daily basis."

"Well, I read mine," Rodney told us with conviction from his work station, "all the way down to the fine print. Sure, there is a hazard pay clause, but I can say with certainty that no where in there did it say save city and everyone in it on a daily basis. And as soon as we get back to Earth, the Human Resources Department is going to get a little visit."

"Rodney!" Dr. Zelenka exclaimed as he came running into the control room, rolls of paper in his hands. "We have been thinking all backwards, we are so stupid."

John moved over to the two men. "Okay, biting my tongue here."

Rodney glared at the Major then turned back to his fellow scientist. "What are you talking about, Radek?"

Dr. Zelenka shook his head, "We have spent all this time trying to stop the virus from spreading, when instead we should be trying to stop city from sinking."

"I thought that was the same thing," Rodney told the Czech, then he turned to me and the Major. "That is the same thing, right?" Then back to Radek, "I'm pretty sure that's the same thing"

"No, no, no." Rodney took a step back from Radek's waving paper tubes. "We have been trying to stop the virus from testing and rewriting computer program that will sink the city. But, the program will no work if it cannot connect to actual systems that will cause the city to submerge."

"That's true, of course, but we don't know how the Ancients actually submerged the city in the first place."

Dr. Zelenka began unrolling the papers he carried, revealing drawings of the lower level of Atlantis. "It was so simple, Rodney, so obvious. Like submarine. They flooded the compartments of lower levels. We even saw signs of water in these levels but we thought it was from shields partially collapsing when we arrived."

"How?" Rodney asked, intrigued.

"The desalinization stations, look, see how they are distributed throughout the city."

The desalinization stations provide potable water for all of Atlantis. They are spread throughout the city, presumably for ease of distribution. The units themselves are quite amazing. Vast airplane hanger sized rooms, with tanks two stories high that bring in millions of gallons of sea water and process it into drinking water.

"Of course," Rodney said, "they are already pumping water in. It would simply be a matter of opening the pumps, sealing the doors and letting them fill. The weight would pull the city down like a submerging submarine."

"Precisely!"

"So, what do we have to do?" John asked and I eagerly awaited the answer.

"We shut down the pumps, cut the power and they won't be able to fill the rooms."

"Can we do that from here?" I asked fearing I knew the answer.

Rodney shook his head. "No, the virus will override any remote instructions we give the pumps from here. We have to physically cut the power at the actual pumps."

"How do we do that," I asked.

"Peter is working problem right now," Radek volunteered. "but it should be simple. Cut proper wire, then pumps work no more."

I looked at the map, "There must be at least twenty stations spread across the entire city."

"Twenty-three, actually," Dr. Zelenka supplied as he pointed at the blueprint, "three on each arm and five here in central hub."

"If we split up, each take a section of the city, we can probably do it before time runs out," John offered.

"Take the jumper," Rodney recommended, "drop off someone at each pier; it will be quicker than walking the entire distance. I'll take the main hub."

We met Dr. Grodin in the lab, where he provided directions and wire cutters. Dr. Zelenka had been correct, once we were able to access the correct panel and identify the correct wiring, the actual snipping would be simple and painless.

We split up then. Rodney heading down to the lower levels of the hub and the rest of us loading into the jumper and heading out to the arms. Peter and Radek were dropped first, taking two arms each, seeing as they would be more familiar with the necessary panels and wiring. Major Sheppard dropped me next before moving to his own assigned section.

"Will you be okay?" he asked.

As ridiculous as it sounded, I understood why he asked his question. As the expedition commander, I had never had a reason to explore the city. Sure I had seen large sections of it, but always after someone else had been through it and never without several consultants pointing out whatever problem I was being brought to see.

"Fine," I assured him. "Like Radek said, cut wire, pumps work no more."

He smiled. "Just give a holler if you need anything. I'll be back to pick you up when I'm done."

I nodded, exited the jumper and was left alone in an unfamiliar part of the city for the first time since my arrival. I entered the hallway, visualizing the map Peter had shown me during our impromptu lesson. After a short walk, I entered the first desalinization room. Like the one I toured in the hub, this one was enormous, and I could hear the midlevel hum of the pumps and tanks processing the water. According to the engineer that gave me the tour, the pumps could move literally thousands of gallons of water a minute. As large as this room was, I could tell that if they were pumping at maximum capacity, even it would be filled in a matter of minutes. I walked across to where the access panel was, opened it easily with the screwdriver I had been given and pulled out a bundle of wires. Peter had made it pretty easy, just cut them all, and let the engineers worry about reconnecting them after this was all over. I took the wire cutters from my pocket, snipped as directed and listened as the drone of the pumps quieted. The entire room was silent and I sat for a few seconds reveling in the absence of noise.

How long had it been since I could consider myself completely alone? Since well before departing Earth. There had actually been less private time in Antarctica than on Atlantis, McMurdo Station is actually a rather bustling base considering it is hanging out at the very bottom of the planet. But even here on Atlantis, I am never truly alone. There is always someone right outside my office needing an approval or requesting an authorization. There is always a briefing to attend or a newly discovered item to inspect. Even my quarters are not sacred as there is no telling when I will be awakened to breakup another scientific tizzy fit. No the silence in the disabled pump room was truly golden, doubly so since it meant we were one snipped wire closer to keeping Atlantis afloat. 'One down, two more to go,' I thought as I stood and with echoing footsteps went in search of the next room.

It took me close to an hour to disable all three stations on my wing and return to the pier. I radioed John and within a few minutes he was there with the jumper to pick me up. He called to Radek and Peter to check there progress. Peter was getting ready to disable his last panel, but Radek had two left.

Rodney came on the radio then, "Radek I'm finished up in the hub, I can be at the innermost station on the Northwest arm in about twenty minutes. Go ahead and take the next one you have then head back to the jumper."

Radek agreed and by the time we had retrieved Peter, he was ready to be picked up himself. The four of us returned to the control room to await Rodney's arrival. We had been back about five minutes when the alarms began to sound again and the doors and windows slammed shut.

"It's reached the quarantine system," Peter informed us.

"Rodney," I called on the radio, "we're in quarantine lockdown up here. Are you still able to access the hallways you need?"

"The door to the stairwell just locked behind me, but there is nothing keeping me from moving through the corridor. I should reach the final station in a few minutes."

After a few minutes more, the alarms quieted, but the doors remained locked. I turned to Radek and Peter with the question of why.

"I don't think it will release the doors until it is finished rewriting the program," Peter suggested.

"Will it start testing the next system, before it finishes the rewrite?" John asked in concern.

"Possibly," Peter responded unassuredly.

"McKay, are you finished, down there?" John called over the radio.

"Just about, I'm in the last room now."

And that's when he said it.

"Oh, no."

"McKay? What's wrong?"

"The doors just sealed shut and the pumps have started."

I feel like I have been punched in the stomach.

"Rodney, get out of there, now." John leans against the control console as he speaks.

"I can't! The doors are sealed!" He is yelling to be heard over the roar of water entering the compartment. "You really need to pay closer attention to what I say."

"Then cut the wires and disable the pumps."

"I don't think you realize the amount of water that is coming through these things, I can't get anywhere near them."

The Major turns and begins walking towards the exit. "Hold tight, I'm coming to get you."

"So now you can walk through walls? The doors are still locked by the quarantine protocol. You can't leave the control room. Besides, you'd never make it. In about thirty seconds, I'll be treading water."

John reaches the door and I can see him try to open it with both his hands and his mind. It doesn't budge. With a growl, he kicks it. He begins to pace, like a caged animal, turns and addresses the two scientists standing with the same shell shocked look that I am sure I wear. "What do I do?"

No one says anything, and then Rodney comes across again. "You leave and take the others with you."

John shakes his head while still pacing. "Not happening, McKay. I won't do that. I can't do that."

"You did it once before, John, you can do it again."

I suddenly know exactly how my alternate self felt when she sat helplessly in that jumper and Rodney and Peter drowned in this very room. I could have lived this entire existence happily never knowing that feeling of powerlessness. Yet here I stand reliving something I never really lived before.

And, the Major, he looks like he's been slapped.

"No, _I_ didn't. That was a different Sheppard and a different McKay. Those two never had plans to go to Vegas. You said it yourself, infinite number of realities, infinite number of decisions. Well, in this reality, I don't leave you to drown and we go hit the buffets."

"You know, you piss me off to no end. The one time you listen to me and you find a way to throw it back in my face."

"What can I say, for once it sounded pretty cool. Now tell me, I know you have something rolling around in that pain in the ass civilian genius brain of yours. What do I do?"

"Nope, sorry Major, I just won't risk it."

John slams his hand on the wall. "God dammit, I am sick of this noble Rodney McKay shit. Now let me talk to your self preservation side. You know, the I hate imminent death, I'm allergic to bee stings, pollen, citrus, and anything that isn't hermetically sealed in a cellophane wrapper Rodney McKay that seems to show his whiney ass on every damned mission we go on."

"Well, since you asked so nicely. No."

John is clenching his fists now. "Let me make this very clear, I am going to get you out of that oversized aquarium if for no other reason than to beat you within an inch of your smug, egotistical life."

"You drive a hard bargain, Major, and as tempting as your offer of bodily harm is, I'm afraid I'll have to pass."

He kicks a chair sending it scooting across the room. "You have got to be kidding me, McKay!" He turns then and tells the three of us flinching away from his red-faced rage. "I swear to God, I am going to pop a vein. I can feel it, right here." He taps repeatedly at the middle of his forehead. He then screams at Rodney, "Do you hear that, you son of a bitch, you are going to be the death of me yet!"

"Actually I'm doing this to save you, all of you."

"I'm doing this to save you," John mocks in a childish voice as he continues to pace. "You're enjoying this aren't you? Getting a big kick out of playing the hero."

"Not in the least." And for the first time I can hear the fear coming through. "I'm actually pretty much hating it, but it has to be done."

John stops walking and leans his forehead against the wall. "We've taken out enough of the pumps so that the city isn't going to sink, you drowning in the last room isn't accomplishing anything good."

"No, but getting me out could do something really bad."

He turns and slides down to the floor, letting his head sink into his hands. "What? What could I possibly do that would kill all of us…." He lifts his face with a gloating sneer and he begins to laugh. "Oh, ho, ho, McKay, I listen more than you give me credit for."

"What? What did I say?"

"Shut down of the entire system," John tells him as he jumps to his feet. "You said if we shut down the entire system it might cause the gate to explode when we restart. But I bet it will also stop those pumps from running."

"Don't even think about it. In fact, don't think at all. Just be a good little fly boy and do what comes naturally and stand around with a vacant stare and even more vacant mind. With that damned gene of yours, you start thinking too much you'll have the whole place glowing blue and that is just too dangerous right now. I will not let you endanger your life and the others just to try to save me."

"I'm sending the others to the jumper. Grodin can fly it, more or less. He can shoot his way out if the jumper bay is still locked down in quarantine. Then it will be just the two of us. My life, my choice, no one else's."

"Stop quoting me to me!"

"Then stop stalling and tell me what to do to lessen the chance of blowing us up."

There is no answer. "McKay, tell me or I just shut down and restart."

"It's more than just blowing up the base, it could destroy the gate and destroy everyone else's chances of getting home."

Radek cut in then, "Rodney, we will be able to fix it, do not worry about such things."

"Uh-uh, too big of a risk."

"Look, if I have to," John offers, "I will fly a jumper out and tow a replacement gate back from orbit somewhere."

"Please! Don't be ridiculous! The closest gate in orbit is light-years away."

"That's okay. I don't have any pressing plans. I can see it now, orange survey flagging streaming behind it, a big ole' 'Wide Load' sign across the opening. Hell, I'll even let you drive another jumper like a pilot car. We'll put a blinking light on it and everything"

Again there is just silence. "McKay? If you don't answer, I'm going to shut it down."

"Are the others gone yet?"

He motions us toward the jumper bay but none of us leave. "They will be before I shut down."

He sighs, "You could try to do what you did on the jumper. Shut everything down then just bring up one system at a time. Just make sure that you don't restart the gate. That will require a certain amount of patience and finesse, something you obviously don't possess."

"This isn't the jumper, Rodney, it's the entire city."

"It's the same principle, Major, just on a larger scale. Aim small, hit big. Try not, do. Just do it. Feel free to insert the inspirational slogan of your choice here."

"I got it, but…I _know_ the jumper, it's like we've bonded."

"I'm happy for you, John, really. As soon as I get out of here you will have to tell me where the two of you are registered. But in case you were really serious about trying to get me out of here, you should know that..e.wat..s…"

A sharp crackling sound comes across the receiver.

"McKay?"

"…dio is short…"

"You're breaking up."

"…ohn, can y...?"

"Rodney?"

"Ouch! ...other fuc..r!"

There is a last buzzing pop.

"Rodney!"

Static.

"Alright, everybody to the jumper. I've got to do this, now." He pushes me toward the two scientists, shooing us to the jumper bay. "If it comes down to it, I'm willing to tell his sister that he died saving a gaggle of small children, but I'll be damned if I have to tell her that his last words were describing the ever popular maternal copulation ritual to a malfunctioning comlink."

From their stance I can tell Peter and Radek have no intention of going anywhere and neither do I, which is exactly what I tell the Major.

"You heard the man, he wants you gone before I try this and so do I."

Peter shakes his head. "There's not time, he could be underwater while we stand here arguing about it."

"Please, just restart one small system." Radek encourages him. "Like doors. Nothing big, nothing fancy. We will be fine."

I nod in agreement. "Do it, John, shut it down."

He swallows, closes his eyes, "He's going to kill me if I get you people killed." He places his hands on the console and says a single word "Off."

With a quite whir the city goes dark and silent. No one speaks, no one moves. I can hear my heart pounding in my chest, filling my ears with the sound of rushing blood. The afternoon sun shines through the stained glass leaving long yellow and red shadows across the floor and I decide it is actually a rather pretty site to be looking at if I am going to die within the next few seconds. John maintains his shut eye stance at the console then says, "Doors." With a swoosh all the doors in the control room slide open. I can hear that same swooshing hum echoing down the hallway. At the sound, John opens one eye and looks around. "We still alive?"

I smile and nod my head. "Looks like."

He releases a breath. "Good, let's go see if the same goes for McKay."

His strides are long and fast, so that the three of us trailing in his wake are moving at a half jog to keep up. It is strange, almost eerie to traverse past door after door standing open to reveal one empty room after another. And it's just not the entry doors. I have no doubt that every one of the thousands of doors in the entire city is ajar at this very moment. And I mean every door; the closets, the cabinets, the bathrooms, the showers, every door that can respond to the ATA gene has swung open at John's command. It looks as if someone was searching so frantically for a cherished lost object that he didn't take the time to even close the doors to the sites he had already searched. In a way, that is exactly the case.

We take the stairway down to the lower level, breaking out our flashlights to see the steps. When we reach the lower level there is standing water at the doorway and I feel the blood drain from my face as I realize how much water it would take to reach from the desalinization station to this point and the force at which it must have been released. John walks through without comment although his frown is obvious and he begins splashing through the small puddles that lead to Rodney's last known location.

Halfway down the hall he stops and he raises a halting hand. We comply with the unspoken order and he tilts his head as if listening. I can hear it now, a slow-moving, lopsided, squishing noise heading our direction. He breaks into a full out sprint, leaving us with no choice but to pursue in the same manner. We round a corner and there stands Dr. Rodney McKay, saturated with seawater, missing one shoe and ringing out his shirt. I let out a relieved sigh at the site of him.

"Hey," he says gulping air like he has just finished running his own footrace. "I don't suppose you have a towel on you."

I'm concerned that the Major's face may split open with his smile. "I think I know where we can find one."

"Good," he says and bends at the waist to let out a cough laced with seawater. John places a hand on his back until he has his breath and can stand almost upright again.

"I, uh, lost a boot. I looked around," Rodney motions twirling hands towards the room that was almost his tomb, takes a breath, before coughing again "for it, but I couldn't find it. I think it must have gotten washed out to sea."

"You're lucky that's all that got washed out to sea."

"It almost wasn't," Rodney says without explanation, but he shivers and I can't tell if it is from the cold water or the memory of his escape.

John puts his arm around his shoulder, rubbing his wet bare arms. Rodney places his hands on his knees and succumbs to another bout of coughing. When he is able to breathe again, he leans heavily into his friend, and although he would never ask for it, I can see how relieved he is to have something strong and stable to support him right now.

"You're not going to puke or anything are you?"

"Took care of that before you got down here." He takes another breath and seems to savor it with closed eyes before continuing. "So, evidently it worked. You shut down the system and the gate didn't blow up?"

"Evidently."

"Wonders never cease." He gulps more air and fights to hold in another cough

John's smile has turned into a concerned scowl. "Look, do you want to sit down?"

He shakes his head. "Easier to breathe standing up."

"This is easy?"

"Compared to earlier, this is heaven." He shivers again and I wish Carson wasn't all the way on the mainland.

"Whatsay, we go find that towel now?" John tells him and with his consenting nod, starts leading him down the hall with his arm still around his shoulders.

"What are they still doing here?" Rodney asks indicating me and the other two scientists grinning like fools behind him.

"Believe it or not I actually found three people that are even bigger pains in the ass than you are."

"That's brilliant civilian genius pain in the ass to you."

"Let's just call it McKay for short."

Rodney can no longer contain the cough and John tightens his grip on his shoulder. He doesn't let up on it until Rodney is safely seated in the jumper and we depart to bring our team home to Atlantis.

"Okay, let's try this again, shall we?" I tell the two men sitting in my office.

There stance is remarkably similar to the last time we were here, same slouch, same tapping foot only this time they both have the annoyed glint in their eyes.

"As I told you before, your work here…"

Rodney cuts me off, "Yes, yes, we're dedicated and exemplary and you're pleased as punch. Now, can we cut to the chase here? Because I've got a ZedPM to find and I can't do that until I get the damned gate fixed."

I look to John and he just shrugs, "What he said."

I glance through the window behind the men and can see the skeleton crew of technicians that have returned to Atlantis. Rodney was adamant that until each system could be checked out, only the bare minimum of personnel necessary to see to the diagnostics and any repairs be allowed to return. I agreed whole heartedly and although I know this meeting is necessary I cannot help but also agree with his need to return to the repairs.

I frown slightly at his outburst then continue. "Very well, as you have already surmised, Dr. Kavanaugh had some rather telling information in his debrief regarding Major Sheppard threatening him with bodily harm and Dr. McKay actually carrying through with the same."

With a deep scowl, Rodney crosses his arms across his chest and slouches into an almost identical position to the one John has been maintaining. John, however, sits up and leans forward. "Did this telling information happen to include why he deserved the ass whooping he recieved?"

I hold up a hand. "John, if anyone on this base knows how tempting it is to threaten and/or beat Dr. Kavanaugh, it is me. However, as I stated previously, you two are my senior advisors and I expect you to maintain a certain amount of restraint. What you did, Major, was unbecoming and unprofessional behavior and I will not abide it from you or Dr. McKay, no matter what the reason."

John resumes his cross-armed slump and I am struck by how similar they look, like inverse negatives of the same image. I take another breath and continue. "Now, that being said, I cannot let this go unpunished." If possible, both frowns deepen.

"Major, seeing as you only threatened the doctor, I am willing to settle for the verbal counseling I have just given you and a note to your record." He starts to speak, but with a disapproving look from me he closes his mouth and sinks deeper into his chair.

"Doctor, your charges are much more serious as you did actually physically assault, Dr. Kavanaugh. As a result, I have no choice but to enforce some sort of confinement as punishment in addition to your own written reprimand." His eyes actually seem to flash with anger but he remains silent. "However, seeing as you spent quite a bit of time sealed inside a desalinization station yesterday, I will consider that time served." Both of them give me cautiously surprised looks.

"Now, if you will excuse me," I tell them as I take the written reprimands and wad them into a small ball of paper, "I need to file this paperwork." I toss them casually into the trashcan.

They exchange wary glances at each other and me before standing. "Are we done?" John asks.

I look back at my file, noting one other item that I was meaning to discuss with them. "Do I have your words that you will be on your best behavior from now on, no matter how infuriating certain people can be?"

Both of them nod eagerly, although the roll of Rodney's eyes does not escape my notice. But if that's the extent of his annoyance I know I have won this little battle. "Then we're done," I tell them as I close the file. I'll save the issue of glowing green surgical gloves flying off balconies and being left to flip off certain annoying scientists for another day.

They leave then and I am left in the relative aloneness that has become the norm here on Atlantis. I know it will be short lived, there is always another question to answer, another procedure to approve. As much as I hate to admit it, this is a bureaucratic system I run here, and I am the head bureaucrat. As such, it my job to make sure the system runs as smoothly as possible. If we were back on Earth, Rodney probably would have received some sort of punishment and John's written reprimand would have made its way into his actual file. But we are not on Earth, not even in the same galaxy, therefore, I allow myself some leeway, some flexibility. Some might consider what I did today favoritism, but I call it survival. The Wraith may not be knocking on our door today, but the time is coming soon and the two men that I thought were valuable assets at the beginning of the mission have become absolutely critical in spite of what I perceived as flaws. No, they are valuable because of those flaws. What I once thought was arrogance I now see as confidence, the disrespect is determination, and the bickering is actually compassion. We will not survive the Wraith without those characteristics and every day I become more convinced we will not survive them without the two men that embody them so well.

And if that means I bend the rules, allow a little more leniency, let them work the system, then so be it. Some would consider the system flawed that allows such actions. So what? So there are bugs in the system. I accept them, welcome them, actually encourage them. I have decided that they don't weaken us, they make us stronger. I'm the head bureaucrat, the top administrator, the mission commander. When the time comes, I am the one that will be responsible for all these people. I am the one that will have to sound the battle cry. The thought chills me like the icy waves that lap at this glorious city we are fighting to save.

But at my core, I am a negotiator and the art of negotiation is being able to convince the person across the table that your negatives are actually positives and your weaknesses are your strengths. Sometimes your arguments are so persuasive that you even convince yourself; whether it is a result of wishful thinking or true conviction, only time will tell. And time is just one more thing of which we are in short supply.


End file.
